Fig. 2

LabPipe setup and workflow in the exemplar EMBER breathomics study. The EMBER LPS was setup to handle standard operating procedures for four analytical chemistry instrument data/sample collection techniques including: proton-transfer-reaction mass spectrometry (PTR-MS); gas chromatography ion mobility spectrometry (GC-IMS); atmospheric pressure chemical ionisation compact mass spectrometry (APCI-CMS) and a breath sampler device which collected samples for later analysis. Re-usable configurations for each technique (shown in the diagram with distinct colours) were setup with data collection forms containing appropriate field processing/validations and data file handlers. Data collection at each site was managed through LPC instances which loaded appropriate configurations to generate metadata forms and guide the user through any manual steps required when saving data files. Once these steps were completed, the LPC automatically uploaded data and metadata to the LPS.